I'm not sure what you mean with "private" DNS. Route53 actually provides a (public) DNS service.
If you have installed boto, you can update DNS settings like this:
DNS_ADDRESS="`ec2metadata | grep 'public-hostname:' | cut -d ' ' -f 2`"
/usr/local/bin/route53 change_record <Hosted zone ID> foo.bar.com. CNAME $DNS_ADDRESS 300
DNS_ADDRESS is the AWS DNS name of the instance. The second line creates a CNAME. You need to add the hosted zone ID of the domain you want to change. If you put this snippet into /etc/rc.local, the instance will automatically update / create the CNAME when it's booting.